8VSJ: Engineered peptide-specific binder

Engineered peptide-specific binder in complex with HLA-DR1/CLIP. Determined by electron microscopy at 2.28 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 2.28 Å
Organisms: Homo sapiens, Metamycoplasma arthritidis
Chains: 6
Atoms: 5,832
Mol. weight: 108.78 kDa
Ligands: NAG
Released: 2 Oct 2024

Explore 8VSJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VSJ contains 20 α-helices and 54 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	1
β-strand	17-24	8	1
β-strand	27-33	7	1
β-strand	38-41	4	1
α-helix	44-48	5
β-strand	51	1	2
α-helix	54-57	4
α-helix	58-74	17
α-helix	78-81	4
β-strand	83	1	3
α-helix	84-85	2
β-strand	86-91	6	4
β-strand	101-110	10	4
β-strand	111	1	3
β-strand	118-121	4	5
β-strand	124-126	3	5
β-strand	131-132	2	4
β-strand	136	1	4
β-strand	143-151	9	4
β-strand	159-163	5	5
β-strand	172-176	5	5

Chain B: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	186-197	12	1
β-strand	202-211	10	1
β-strand	214-220	7	1
β-strand	225-228	4	1
α-helix	234-240	7
α-helix	244-251	8
α-helix	253	1
α-helix	254-259	6
α-helix	260-265	6
β-strand	274	1	6
β-strand	277-283	7	7
β-strand	292-301	10	7
β-strand	302	1	6
β-strand	308-312	5	8
β-strand	315-317	3	8
β-strand	321-323	3	7
β-strand	327-328	2	7
β-strand	334-340	7	7
β-strand	350-354	5	8
α-helix	362	1
β-strand	363-367	5	8

Chain C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	24-25	2
α-helix	26-34	9
α-helix	42-65	24
α-helix	69-88	20
α-helix	93-119	27

Chain H: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	18-25	8	9
β-strand	32-39	8	10
β-strand	46-51	6	10
β-strand	57-59	3	10
β-strand	67-72	6	9
β-strand	77-82	6	9
α-helix	84-86	3
β-strand	88-96	9	10
α-helix	100C	1
β-strand	100D-103	4	10
β-strand	107-109	3	10

Chain L: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	44-46	3	12
β-strand	48-49	2	13
β-strand	53-54	2	13
β-strand	62-67	6	11
β-strand	70-75	6	11
β-strand	85-90	6	12
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-106	5	12

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	184	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen DR beta chain	B	protein	192	Homo sapiens	D7RIG0 (AlphaFold model)
Superantigen	C	protein	129	Metamycoplasma arthritidis	Q48898 (AlphaFold model)
c44H10 Fab heavy chain	H	protein	223	Homo sapiens
c44H10 Fab light chain	L	protein	214	Homo sapiens
Class-II-associated invariant chain peptide	P	protein	15	Homo sapiens	P04233 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8VSJ_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DASR

Sequence of entity 2 (B), FASTA

>8VSJ_2 HLA class II histocompatibility antigen DR beta chain (chains B)
GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVS
GFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSV
TSPLTVEWRASR

Sequence of entity 3 (C), FASTA

>8VSJ_3 Superantigen (chains C)
MKLRCENPKKASIYLAQNLNNVVFTNKELEDIYDLSNKEETKEVLKKFKEKVNQFYRHAF
DIINKYGDKEVFNMMFLKLSVVFDIQRKEANNVEQIKRNIATLDEIMAKADNDLCYFISQ
WLEHHHHHH

Sequence of entity 4 (H), FASTA

>8VSJ_4 c44H10 Fab heavy chain (chains H)
QVQLKESGPGLVAPSQSLSITCTVSGFSLTSYGVHWVRQPPGKGLEWLGVIWAGGSINYN
SALMSRLSISKDNFKSQVFLKMSSLQTDDTAMYYCARAYGDYVHYAMDYWGQGTSVTASS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 5 (L), FASTA

>8VSJ_5 c44H10 Fab light chain (chains L)
DIQMTQSPSSLSASLGQRVSLTCRASQEISGYLTWLQQKPDGTIKRLVYAASTLDSGVPK
RFSGSRSGSDYSLTISSLESEDFADYYCLQYTNYPLTFGAGTKLELKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 6 (P), FASTA

>8VSJ_6 Class-II-associated invariant chain peptide (chains P)
PVSKMRMATPLLMQA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

A general system for targeting MHC class II-antigen complex via a single adaptable loop. Du, H., Liu, J., Jude, K.M. et al. Nat Biotechnol (2025) 43:1673-1682. DOI 10.1038/s41587-024-02466-y · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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